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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
Allaband Lab
About me
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Posts
Future Blog Post
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Blog Post number 4
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Blog Post number 3
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Blog Post number 1
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mentees
Maria Tiu
I mentored Maria (Denalene) during her undergraduate and Master’s program. She is now an MD in Fresno, CA! LinkedIn
Tanya Kumar
I mentored Tanya during her graudate (MD/PhD) program. LinkedIn
outreach
Fermentation and Digestion. Permalink
Published:
How do microbes influence food and human health? Students identify relationships between the microbiome and health through their own cultural lens.
Letters to a Pre-scientist Permalink
This organization pairs middle schoolers with scientists, engineers, and technologists from around the world through snail mail. These personal connections shatter stereotypes, spark curiosity, and help students see themselves in a STEM career - sometimes for the very first time.
Digestion and Fermentation
Published:
Dr. Allaband will be talking about how the collection of bacteria and other microscopic creatures of the gut microbiome can help both animals and people digest their food and stay healthy. She will cover a variety of different topics - including probiotics, different ways animals digest their food, how diet impacts health, and debunk an animal myth or two.
Microbial Magic: How Microbes Shape Human and Animal Health
Published:
The microbes in your gut may seem to be very mysterious and we know they can have a powerful effect on your health. While it may seem like magic, scientists are learning more every day about microbes and the molecules they use to send messages to our bodies. This is also true for our pets and their health as well.
publications
Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales.
Published in Drug Discovery Today: Disease Models, 2018
In this perspective, we examine how the microbiome influences gastrointestinal disorders, metabolic dysregulation, reproduction, and disease susceptibility in captive wildlife. Investigation of wildlife, and specifically captive wildlife, affords a unique opportunity to gain understanding of the broad diversity of the associated microbiota and learn from nature’s molecular and microbial responses to disease.
Recommended citation: Williams, et al. (2024). "Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales.." Drug Discovery Today: Disease Models. 2018 Jun 1;28:105-15. https://doi.org/10.1016/j.ddmod.2019.08.012
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.
Published in Clinical gastroenterology and hepatology, 2019
Overview of clinical applications of human microbiome research - its pitfalls, limitations, and future promises
Recommended citation: Allaband, et al. (2019). "Microbiome 101: studying, analyzing, and interpreting gut microbiome data for clinicians.." Clinical gastroenterology and hepatology. 17(2), 218-230. https://doi.org/10.1016/j.cgh.2018.09.017
Human skin, oral, and gut microbiomes predict chronological age.
Published in Msystems, 2020
This study sets the stage for future research on the role of the microbiome in accelerating or decelerating the aging process and in the susceptibility for age-related diseases.
Recommended citation: Huang, et al. (2020). "Human skin, oral, and gut microbiomes predict chronological age.." Msystems, 5(1):10-128. https://doi.org/10.1128/msystems.00985-24
How the gut microbiome affects distal organs.
Published in Hills Global Symposium 2024, 2020
These proceedings discuss how the microbiome can affect additional organs in the host body.
Recommended citation: Allaband and Knight. (2024). "How the gut microbiome affects distal organs.." Hills Global Symposium.
Intermittent hypoxia and hypercapnia alter diurnal rhythms of luminal gut microbiome and metabolome.
Published in Msystems, 2021
We found changes in microbial families and metabolites during different parts of the day that regulate many metabolic pathways contributing to the increased risk for heart disease seen in patients with obstructive sleep apnea.
Recommended citation: Allaband, et al. (2021). "Intermittent hypoxia and hypercapnia alter diurnal rhythms of luminal gut microbiome and metabolome.." Msystems, 6(3):10-128. https://doi.org/10.1128/msystems.00116-21
Compositionally aware phylogenetic beta-diversity measures better resolve microbiomes associated with phenotype.
Published in Msystems, 2022
We show using simulated and real data that our new methods provide improved classification accuracy of ordinal sample clusters and increased effect size between sample groups on beta-diversity distances.
Recommended citation: Martino, et al. (2022). "Compositionally aware phylogenetic beta-diversity measures better resolve microbiomes associated with phenotype.." Msystems, 7(3):e00050-22. https://doi.org/10.1128/msystems.00050-22
Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing.
Published in Journal of Applied Microbiology, 2024
Fecal microbiota transplantation holds promise in dolphin medicine as a therapeutic tool to restore healthy gut microbiota without antibiotic use.
Recommended citation: Linnehan, et al. (2024). "Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing.." Journal of Applied Microbiology, Volume 135, Issue 2, February 2024, lxae026. https://doi.org/10.1093/jambio/lxae026
Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus).
Published in Journal of Applied Microbiology, 2024
Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease.
Recommended citation: Tang-Wing, et al. (2024). "Impact of diet change on the gut microbiome of common marmosets (Callithrix jacchus).." Msystems, Aug 20;9(8):e00108-24. https://doi.org/10.1128/msystems.00108-24
The changing metabolic landscape of bile acids – keys to metabolism and immune regulation.
Published in Nature reviews Gastroenterology & hepatology, 2024
Existing bile acids, both host and microbial-derived, have been shown to serve as agonists for multiple transcription factors and receptors, which is discussed extensively in this Perspective.
Recommended citation: Mohanty, et al. (2024). "The changing metabolic landscape of bile acids–keys to metabolism and immune regulation.." Nature reviews Gastroenterology & hepatology. Jul;21(7):493-516. https://doi.org/10.1038/s41575-024-00914-3
Time of sample collection is critical for the replicability of microbiome analyses.
Published in Nature Metabolism, 2024
We argue that not controlling for host circadian rhythm time is like trying to measure sea level rise without understanding that tides exist.
Recommended citation: Allaband, et al. (2024). "Time of sample collection is critical for the replicability of microbiome analyses.." Nature Metabolism. 6, 1282–1293. https://doi.org/10.1038/s42255-024-01064-1
Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.
Published in Msystems, 2024
Using barcoded Matrix Tubes, we show a significant reduction in cross-contamination compared to conventional plate-based approaches; this innovation improves large-scale study design by shortening processing times, simplifying analysis, facilitating metadata curation, and producing more reliable results.
Recommended citation: Brennan, et al. (2024). "Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.." Msystems, 9(10):e00985-24. https://doi.org/10.1128/msystems.00985-24
talks
Microbiome 101 for veterinarians: Fecal transplantation, microbiome analysis, and more (Part 1 and 2).
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Discussed the fundamentals of the microbiome and how it impacts clinical practice, including antibiotics, probiotics, and fecal transplantation. The basics of microbiome analysis were also discussed.
Multiomic Analyses Lead to Breakthroughs in Medicine
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Discussed how multiomic analyses lead to breakthroughs in veterinary medicine
Impact of the Gut Microbiome on Circadian Rhythms and Health
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Presented evidence of how host circadian rhythms could impact the microbiome, which in turn affects metabolism and health.
Talking to Your Gut Bacteria: Circadian Rhythms and Signaling Molecules
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Discussed how bacterial genes, like bsh, modify host created bile acids in ways that changes the signaling in host receptors, which in turn affects health and disease.
Time of Sample Collection Critical for Microbiome Replicability
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Presented recent findings on how host circadian rhythms could impact the interpretation of microbiome results, making time of sample collection a critical parameter for microbiome replicability. Recording
Engineered Native E. coli Strain Outperforms Engineered Non-Native Strain in Conventionally-Raised Murine Gut over 10 Months
Published:
Presented preliminary data on how an engineered host-native bacteria was better able to engraft and function long term inside that host than a non-host-native engineered bacteria.
Diet Change Improves Physiological Parameters and Significantly Impacts the Microbiome and Metabolome of the Common Marmoset
Published:
Presented preliminary data on how captive laboratory marmosets microbiome (shotgun metagenomics) and metabolome (untargeted LC-MS/MS) responded to dietary change.
Dietary-Induced Changes in the Gut Microbiome and Metabolome Correlate with Improved Clinical Parameters in the Common Marmoset
Published:
Presented preliminary data on how captive laboratory marmosets microbiome (shotgun metagenomics) and metabolome (untargeted LC-MS/MS) responded to dietary change. Postdoc Poster Prize Winner!
Dry Kibble Diet Has a Distinct Microbiome Composition Linked to Metabolic Disease in Healthy Domestic Cats
Published:
Presented preliminary data on how there is a significant difference between cat microbiomes on wet and dry formulated foods and the implications for host health.
teaching
Animal Microbiome Lecture
Undergraduate course, University of California San Diego, Scripps Institution of Oceanography, 2014
1 hour guest lecture for this freshman seminar course run by Jack Gilbert and Sarah M. Allard
Carpentries Certified Python Instructor
Multiple Workshops, University of California San Diego, 2025
A Carpentries-Certified Python Instructor
A Carpentries-certified Python instructor combines subject-matter knowledge with a strong foundation in educational best practices. The training and certification process focuses on teaching people how to teach, rather than just knowing the content.
Key Aspects of the Teaching Experience
- Evidence-Based Teaching Practices: A central pillar of the Carpentries approach is the use of evidence-based teaching. Instructors are trained in educational psychology principles like managing cognitive load, creating an inclusive learning environment, and using formative feedback. This means they’re not just demonstrating code, but actively thinking about how learners are processing information and how to make the material stick.
- Live-Coding and Hands-on Learning: Carpentries workshops are highly interactive. Instructors lead live-coding sessions where they write code in real-time, explain their thought process, and make deliberate mistakes to show learners how to debug. The hands-on format encourages learners to follow along and practice new skills immediately.
- Inclusive and Welcoming Environment: A Carpentries instructor is trained to create a positive and inclusive classroom. They use practices like the Code of Conduct to ensure a respectful and safe space for all participants, regardless of their background or level of experience. They’re also taught to be mindful of and adapt to different learning styles and needs.
- Team-Teaching: Workshops are typically taught by a team of two lead instructors and several “helpers.” This collaborative model provides several benefits:
- Reduces Instructor Burden: Instructors can share the teaching load, allowing for breaks and fresh energy.
- Provides Real-time Support: Helpers circulate the room (or breakout rooms in virtual workshops) to provide one-on-one assistance to learners who get stuck, preventing them from falling behind.
- Models Collaboration: It demonstrates the value of working together in a scientific or data-intensive environment.
- Teaching Foundational Skills: The focus is on fundamental, reproducible research skills, not advanced topics. For a Python workshop, this might mean teaching concepts like data types, loops, conditionals, and working with libraries like Pandas for data analysis. The goal is to give learners a strong base from which they can continue to learn on their own.
- Volunteer-based and Community-Driven: Most Carpentries instructors are volunteers who are passionate about sharing their skills. They are part of a global community of practice. This provides an ongoing support network where they can connect with other instructors, share experiences, and get advice. The community also maintains the curriculum, which is open-source and collaboratively developed.
- Continuous Improvement: Teaching with the Carpentries isn’t a one-and-done event. Instructors are encouraged to continually develop their skills. After each workshop, they gather feedback from learners and their co-instructors to reflect on their performance and identify areas for improvement. This process of self-assessment and community feedback is a core part of the experience. In essence, a Carpentries-certified Python instructor’s experience is less about being a coding virtuoso and more about being an effective, empathetic, and collaborative educator who empowers others to learn and build confidence with computational tools. —
Dr. Allaband has been a Python Instructor for the following Workshops:
- Annual Fall UCSD Workshop - Sept 15-25, 2025
- Annual Spring UCSD Workshop - May 6-9, 2025
- Fall UCSD Workshop - Nov 12-15, 2024
- Annual Fall UCSD Workshop - Sept 11-21, 2023